docs: def hmmalign_sequences(self, hmm, sequences, output_file):
          '''Run hmmalign and convert output to aligned fasta format
  
          Parameters
          ----------
          hmm: str
              path to hmm file
          sequences: str
              path to file of sequences to be aligned
          output_file: str
              write sequences to this file
  
          Returns
          -------
          nothing
          '''
  
          cmd = 'hmmalign --trim %s %s' % (hmm, sequences)
          output = extern.run(cmd)
          with open(output_file, 'w') as f:
              SeqIO.write(SeqIO.parse(StringIO(output), 'stockholm'), f, 'fasta')